How to select leaves on a sapling-addon tree when selecting their branch?
The leaves can be connected to the sapling mesh through the following steps.

1) In object mode, select the tree and the leaves. 



2) Press ctrl+J to join the meshes.



3) Enter edit mode and select all using A.



4) Press ctrl+F and select 'Intersect (knife)' and make sure the Separate option is unselected and the Source is 'Self intersect'.



5) Now the mesh is fully connected, including leaves. Selecting a vertex and using ctrl+numpad + will select all of the connected elements.